PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq.

ABSTRACT:

Background

Peptide identification based upon mass spectrometry (MS) is generally achieved by comparison of the experimental mass spectra with the theoretically digested peptides derived from a reference protein database. Obviously, this strategy could not identify peptide and protein sequences that are absent from a reference database. A customized protein database on the basis of RNA-Seq data is thus proposed to assist with and improve the identification of novel peptides. Correspondingly, development of a comprehensive pipeline, which provides an end-to-end solution for novel peptide detection with the customized protein database, is necessary.

Results

A pipeline with an R package, assigned as a PGA utility, was developed that enables automated treatment to the tandem mass

SUBMITTER: Wen B 

PROVIDER: S-EPMC4912784 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature